ClinVar Miner

Submissions for variant NM_022829.6(SLC13A3):c.1016+3A>G

gnomAD frequency: 0.00078  dbSNP: rs199961976
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001869054 SCV002299664 uncertain significance not provided 2024-01-19 criteria provided, single submitter clinical testing This sequence change falls in intron 7 of the SLC13A3 gene. It does not directly change the encoded amino acid sequence of the SLC13A3 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs199961976, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with SLC13A3-related conditions. ClinVar contains an entry for this variant (Variation ID: 625426). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
CeGaT Center for Human Genetics Tuebingen RCV001869054 SCV004042133 likely pathogenic not provided 2023-09-01 criteria provided, single submitter clinical testing SLC13A3: PM2, PM3, PP3, PS3:Supporting
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000767378 SCV004171241 likely pathogenic Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate 2023-11-30 criteria provided, single submitter clinical testing
OMIM RCV000767378 SCV000897949 pathogenic Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate 2019-04-12 no assertion criteria provided literature only

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